PhyDesign specifications

Information


Unique identifier OMICS_13194
Name PhyDesign
Interface Web user interface
Restrictions to use None
Input data PhyDesign reads aminoacid and DNA alignments and trees.
Input format NEXUS, FASTA, PHYLIP, NEWICK
Output data Spreadsheet outputs are offered as downloads: a compressed file containing individual rate files for each locus, and a single file containingrate site vectors for all loci. The second result provided is a graphical representation of phylogenetic informativeness and calculations of quantitative measures of informativeness. Two graphs are shown in the main section: the ultrametric tree and, aligned to it, the phylogenetic informativeness profiles.
Output format SVG
Programming languages Javascript, Perl
Computer skills Basic
Stability Stable
Maintained Yes

Documentation


Maintainer


  • person_outline Francesc López-Giráldez <>

Publication for PhyDesign

PhyDesign in publications

 (14)
PMCID: 5599551
PMID: 28912548
DOI: 10.1038/s41598-017-11804-x

[…] regions and cpg islands were identified using the geneious software. the geneious environment was also used to perform dot plot analysis., phylogenetic informativeness (pi) was estimated using phydesign server, . pi profiles were plotted with reference to an uncalibrated tree. the tree used to overlay the historic changes in substitution rates was obtained with maximum likelihood method […]

PMCID: 5790136
PMID: 28595363
DOI: 10.1093/sysbio/syx051

[…] jukes–cantor—highly uneven base frequencies would mean a reduction in effective state space) and the sequence length. a combination of bash scripts and a perl script provided by the authors (http://phydesign.townsend.yale.edu/instructions.html) was employed to obtain an estimate for the potential excess support for the true relationship (for definitions of the terms, see ). this approach […]

PMCID: 5372842
PMID: 28367371
DOI: 10.7717/peerj.3120

[…] condensed trees with a 90% bootstrap cut-off value. this allows us to measure how adding/removing a locus to/from the multiple alignments causes the resulting phylogenetic tree to change., we used phydesign () to establish the informativeness of the various combinations of loci alignments, as described in . we also manually analyzed all trees to identify all cases where isolates […]

PMCID: 5036811
PMID: 27668729
DOI: 10.1371/journal.pone.0163529

[…] sites were calculated together with the homoplasy and retention indices (respectively hi and ri–) using paup* 4.0. a phylogenetic informativeness profile (pi) was obtained for each gene using phydesign [], an on-line program developed from a previous study []. substitution rates for each position were calculated using hyphy implemented in phydesign, selecting a k2p model (base frequencies […]

PMCID: 5010914
PMID: 27503296
DOI: 10.1093/gbe/evw187

[…] of , i.e., type = 8. trees were graphically edited using the software phylowidget () and dendroscope 3.3.2 ()., phylogenetic informativeness (pi) was investigated on the amino acid dataset using the phydesign portal () and rate4site () to estimate site-specific evolutionary rates. best-fitting amino acid evolutionary models were selected using prottest 3.4 () and phyml (). pi was computed […]


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PhyDesign institution(s)
Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA

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